Dataset Information

Dynamics of Early Establishment of SARS-CoV-2 VOC Omicron Lineages in Minas Gerais, Brazil.

ABSTRACT: Brazil is one of the nations most affected by Coronavirus disease 2019 (COVID-19). The introduction and establishment of new virus variants can be related to an increase in cases and fatalities. The emergence of Omicron, the most modified SARS-CoV-2 variant, caused alarm for the public health of Brazil. In this study, we examined the effects of the Omicron introduction in Minas Gerais (MG), the second-most populous state of Brazil. A total of 430 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples from November 2021 to June 2022 from Belo Horizonte (BH) city were sequenced. These newly sequenced genomes comprise 72% of all previously available SARS-CoV-2 genomes for the city. Evolutionary analysis of novel viral genomes reveals that a great diversity of Omicron sublineages have circulated in BH, a pattern in-keeping with observations across Brazil more generally. Bayesian phylogeographic reconstructions indicate that this diversity is a product of a large number of international and national importations. As observed previously, São Paulo state is shown as a significant hub for viral spread throughout the country, contributing to around 70% of all viral Omicron introductions detected in MG.

SUBMITTER: de Menezes MT

PROVIDER: S-EPMC9962645 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

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Dynamics of Early Establishment of SARS-CoV-2 VOC Omicron Lineages in Minas Gerais, Brazil.

de Menezes Mariane Talon MT Moreira Filipe Romero Rebello FRR Whittaker Charles C Santos Franciele Martins FM Queiroz Daniel Costa DC Geddes Victor V Fonseca Paula Luize Camargos PLC de Jesus Jaqueline Góes JG Mendes-Oliveira Franciane F Reis-Souza Valquíria V Santos Bibiana B Zauli Danielle Alves Gomes DAG de Lima Aline Brito AB de Brito Mendonça Cristiane C Alvim Luige Biciati LB do Prado Silva Joice J Malta Frederico Scott Varella FSV de Souza Ferreira Alessandro Clayton AC Faria Nuno R NR Sabino Ester Cerdeira EC Aguiar Renato Santana RS

Viruses 20230220 2

Brazil is one of the nations most affected by Coronavirus disease 2019 (COVID-19). The introduction and establishment of new virus variants can be related to an increase in cases and fatalities. The emergence of Omicron, the most modified SARS-CoV-2 variant, caused alarm for the public health of Brazil. In this study, we examined the effects of the Omicron introduction in Minas Gerais (MG), the second-most populous state of Brazil. A total of 430 Severe Acute Respiratory Syndrome Coronavirus 2 ( ...[more]

PMID: 36851799

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Project description:BackgroundThe pandemic caused by SARS-CoV-2 has not only affected humans but also raised concerns about its transmission to wild animals, potentially creating natural reservoirs. Understanding these dynamics is critical for preventing future pandemics and developing control strategies. This study aims to investigate the presence of SARS-CoV-2 in wild mammals at the Belo Horizonte Zoo in Brazil, analyzing the virus's evolution and zoonotic potential.MethodsThe study was conducted at the Belo Horizonte Zoo, Minas Gerais, Brazil, covering a diverse population of mammals. Oropharyngeal, rectal, and nasal swabs were collected from 47 captive animals between November 2021 and March 2023. SARS-CoV-2 presence was determined using RT-PCR, and positive samples were sequenced for phylogenetic analysis. Consensus genomes were classified using Pangolin and NextClade tools, and a maximum likelihood phylogeny was inferred using IQ-Tree.ResultsOf the 47 animals tested, nine (19.1%) were positive for SARS-CoV-2. Positive samples included rectal, oropharyngeal, and nasal swabs, with the highest positivity in rectal samples. Three genomes were successfully sequenced, revealing two variants: VOC Alpha in a maned wolf (Chrysocyon brachyurus) and a fallow deer (Dama dama), and VOC Omicron in a western lowland gorilla (Gorilla gorilla gorilla). Phylogenetic analysis indicated potential human-to-animal transmission, with animal genomes clustering close to human samples from the same region.ConclusionsThis study highlights the presence of SARS-CoV-2 in various wild mammal species at the Belo Horizonte Zoo, emphasizing the virus's zoonotic potential and the complexity of interspecies transmission. The detection of different variants suggests ongoing viral evolution and adaptation in new hosts. Continuous monitoring and genomic surveillance of SARS-CoV-2 in wildlife are essential for understanding its transmission dynamics and preventing future zoonotic outbreaks. These findings underscore the need for integrated public health strategies that include wildlife monitoring to mitigate the risks posed by emerging infectious diseases.

Project description:The emergence and widespread circulation of severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) or interest impose an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants co-circulation and turnover events has been recorded with the emergence and spread of VOC Gamma in Manaus in late 2020. In this context, we present a genomic epidemiology investigation based on samples collected between December 2020 and May 2021 in the second major Brazilian metropolis, Rio de Janeiro. By sequencing 244 novel genomes through all epidemiological weeks in this period, we were able to document the introduction and rapid dissemination of VOC Gamma in the city, driving the rise of the third local epidemic wave. Molecular clock analysis indicates that this variant has circulated locally since the first weeks of 2021 and only 7 weeks were necessary for it to achieve a frequency above 70 per cent, consistent with rates of growth observed in Manaus and other states. Moreover, a Bayesian phylogeographic reconstruction indicates that VOC Gamma spread throughout Brazil between December 2020 and January 2021 and that it was introduced in Rio de Janeiro through at least 13 events coming from nearly all regions of the country. Comparative analysis of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) cycle threshold (Ct) values provides further evidence that VOC Gamma induces higher viral loads (N1 target; mean reduction of Ct: 2.7, 95 per cent confidence interval = ± 0.7). This analysis corroborates the previously proposed mechanistic basis for this variant-enhanced transmissibility and distinguished epidemiological behavior. Our results document the evolution of VOC Gamma and provide independent assessment of scenarios previously studied in Manaus, therefore contributing to the better understanding of the epidemiological dynamics currently being surveyed in other Brazilian regions.

Dataset Information

Dynamics of Early Establishment of SARS-CoV-2 VOC Omicron Lineages in Minas Gerais, Brazil.

Publications

Dynamics of Early Establishment of SARS-CoV-2 VOC Omicron Lineages in Minas Gerais, Brazil.

Similar Datasets

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